[gmx-users] convert xtc to ASCII file

Justin Lemkul jalemkul at vt.edu
Wed Mar 23 19:19:38 CET 2016

On 3/23/16 2:15 PM, Athina Meletiou wrote:
> Hello all,
> I've been wondering if there is a way to convert a Gromacs xtc trajectory to a plain text file. I've tried Openbabel as it appears to be possible but unfortunately it crashes without a warning. Is there maybe a Gromacs tool that can do the conversion?
> Also, as I'm interested in writing only the carbon atoms and not the hydrogens, I've looked at trjconv to see if I could at least do the selection of atoms using that, as it's specified in trjconv's manual that it can select a subset of atoms. However I've been looking at how to do that but I can't find it in the help menu of the program, so  I was wondering if it's not as straightforward as just selecting a subset of atoms through trjconv and maybe it can olny be done after writing a suitable index file?

Yes, this is exactly the function of an index file.  trjconv can output the .xtc 
contents in, e.g. a multi-frame PDB file by choosing that as the output type.


> Any hints would be greatly appreciated :)
> Thank you all very much in advance.
> Best regards,
> Athina
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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